def main():
p = enz.protein('../data/4key.pdb')
p.mutate(44, 'Q')
p.refold()
print(p.df)
def main():
df = pd.read_csv('test_data/ManchesterSmiles.csv', index_col=0)
p = enz.protein('../data/4key.pdb',
seq=bm3_wt,
key_sites=[82, 87, 330],
cofactors=['HEM'])
failures = []
for i in tqdm(df['Smiles']):
try:
p.dock(i, exhaustiveness=2)
except Exception as e:
failures.append(i)
pd.Series(failures).to_csv('failures.csv')
def evaluate(gene):
mutation_dictionary = dict(zip(TARGET_SITES, gene))
p = enz.protein(
'4KEY.pdb',
seq=BM3_DM, # my residue numbering system
cofactors=['HEM']) # keep the heme
for pos in mutation_dictionary:
aa = mutation_dictionary[pos]
p.mutate(pos, aa)
p.refold()
docking_results = p.dock(
'CCS(=O)(=O)C1=C(N2C=CC=CC2=N1)S(=O)(=O)NC(=O)NC3=NC(=CC(=N3)OC)OC',
target_residues=TARGET_SITES,
exhaustiveness=1)
return score(p, docking_results)
def main(args):
l = []
for i in tqdm(args):
try:
p = enz.protein(os.path.join(i, 'clean_receptor.pdb'), cofactors = ['HEM'])
poses = [enz.mol(os.path.join(i, j)) for j in os.listdir(i) if 'vina' in j]
scores = pd.read_csv(os.path.join(i, 'scores.csv'),index_col=0)
scores['mode'] = scores['mode'].astype(int)
x = get_info(p, poses, scores).reset_index()
x['name'] = os.path.basename(i)
l.append(x)
except:
print('error',i)
df = pd.concat(l)
df.reset_index(inplace=True,drop=True)
df.to_csv('vina-info.csv')
print(df)
def main():
p = enz.protein('4KEY.pdb',
seq = BM3_DM,
cofactors = ['HEM'],
key_sites = [82, 87, 400, 49, 51, 181, 188, 263, 330])
r1 = p.dock(PIOGLITAZONE)
r1.save('DM')
p.mutate(75,'W')
p.refold()
r2 = p.dock(PIOGLITAZONE)
r2.save('DM_L75W')
p.mutate(188,'S')
p.refold()
r3 = p.dock(PIOGLITAZONE)
r3.save('DM_L75W_L188S')
p.mutate(75, 'L')
p.refold()
r4 = p.dock(PIOGLITAZONE)
r4.save('DM_L188S')
def main():
p = enz.protein('../benchmark/data/2UWH.pdb', cofactors=['HEM', 'PLM'])
print(p.df['residue_name'].unique())
p.save('test.pdb')
def main():
p = enz.protein('../data/1jme.pdb')
enz.folds.init()
pose = enz.folds.getpose(p.struc)
print(enz.folds.fold_ccd(pose, {44:'Q'}))